[gmx-developers] Exclude specific nonbonded interactions during md rerun for Verlet

Bernd Doser bernd.doser at h-its.org
Fri Sep 12 17:29:55 CEST 2014

Hi Berk,

thanks for your answer. We store force contributions between two atoms
to analyze them. This storage will be performed during a rerun. We want
to exclude the unneeded interactions to speed-up the rerun, since we are
only interested in forces between two atom groups.


On 09/12/2014 04:21 PM, Berk Hess wrote:
> Hi,
> Why do you need to exclude energy group interactions during rerun?
> Since you will have all the energy group pair contributions you can 
> manually subtract the terms you want to exclude. You wouldn't even need 
> a rerun for that if you used the energy groups for the production run.
> Cheers,
> Berk
> On 09/12/2014 03:26 PM, Bernd Doser wrote:
>> Dear GROMACS developers,
>> As the energy group exclusions are not implemented for the Verlet cutoff
>> scheme, I am search for a alternative possibility to exclude specific
>> nonbonded interactions during an md rerun.
>> One idea is to use the topology exclusion list. The top->excl arrays
>> could be modified for example at the beginning of do_force() in
>> sim_util.c. I have tested it for a small protein and a water dimer and
>> it works. Is there any problem doing this for more complex structures or
>> have anyone a better idea to exclude nonbonded interactions to reduce
>> computation time?
>> Thank you very much in advance!
>> Best regards,
>> Bernd Doser

Dr. Bernd Doser
Software Developer

Schloss-Wolfsbrunnenweg 35
69118 Heidelberg

Phone: +49 6221 533 249
Fax: +49 6221 533 298
E-Mail: bernd.doser at h-its.org
Online: www.h-its.org

More information about the gromacs.org_gmx-developers mailing list